@@ -94,8 +94,7 @@ lineagespot <- function(vcf_fls = NULL,

     lineage_report <- uniq_variants(hits_table = hits_table,

                                    AF_threshold = AF_threshold,

                                    file.out = paste0("lineage_report_",

-                                                     file.out.index, ".txt"),

-                                   print.out = print.out)

+                                                     file.out.index, ".txt"))

     out <- list("variants.table" = vcf_table,

                "lineage.hits" = hits_table,

@@ -28,7 +28,7 @@

 #' merge_vcf(vcf_folder = system.file("extdata",

 #'                                    "vcf-files",

 #'                                    package = "lineagespot"),

-#'

+#' 

 #'           gff3_path = system.file("extdata",

 #'                                   "NC_045512.2_annot.gff3",

 #'                                   package = "lineagespot"))

@@ -50,8 +50,8 @@ merge_vcf <- function(vcf_fls = NULL,

     if( is.null(vcf_fls) ) {

         vcf_fls <- list.files(vcf_folder,

-        pattern = "vcf",

-        full.names = TRUE)

+                              pattern = "vcf",

+                              full.names = TRUE)

     }

@@ -233,7 +233,7 @@ compute_AF <- function(x) {

 change_AA_abbreviations <- function(x) {

-    AA_abbreviations <- data.table(Three_Letter <- c("Ala",

+    AA_abbreviations <- data.table(Three_Letter = c("Ala",

                                                    "Arg",

                                                    "Asn",

                                                    "Asp",

@@ -254,7 +254,7 @@ change_AA_abbreviations <- function(x) {

                                                    "Tyr",

                                                    "Val"),

-                                  One_Letter <- c("A",

+                                  One_Letter = c("A",

                                                  "R",

                                                  "N",

                                                  "D",

@@ -282,8 +282,8 @@ change_AA_abbreviations <- function(x) {

     for(i in seq_len(nrow(AA_abbreviations))) {

         x$AA_alt <- str_replace_all(x$AA_alt,

-        AA_abbreviations[i,]$Three_Letter,

-        AA_abbreviations[i,]$One_Letter)

+                                    AA_abbreviations[i,]$Three_Letter,

+                                    AA_abbreviations[i,]$One_Letter)

     }

@@ -316,7 +316,7 @@ correct_Orf1ab_gene <- function(x, genes) {

 read_gene_coordinates <- function(gff_path) {

-    gene_annot - fread(gff_path, header = FALSE, sep = "\t")

+    gene_annot <- fread(gff_path, header = FALSE, sep = "\t")

     gene_annot <- gene_annot[, c(4, 5, 9), with = FALSE]

@@ -11,8 +11,7 @@ lineagespot(

   ref_folder = NULL,

   voc = c("B.1.617.2", "B.1.1.7", "B.1.351", "P.1"),

   AF_threshold = 0.8,

-  file.out.index = Sys.Date(),

-  print.out = FALSE

+  file.out.index = Sys.Date()

 )

 }

 \arguments{

@@ -30,9 +29,6 @@ that will be integrated into a single table}

 \item{AF_threshold}{A parameter indicating the AF threshold for identifying variants per sample}

 \item{file.out.index}{A string index that is going to be contained in the output file names}

-

-\item{print.out}{Logical value indicating if the produced table should be printed.

-Default value is FALSE.}

 }

 \value{

 A list of three elements;

@@ -51,7 +47,7 @@ variant(s) file(s)

 }

 \examples{

-results = lineagespot(vcf_folder = system.file("extdata", "vcf-files",

+results <- lineagespot(vcf_folder = system.file("extdata", "vcf-files",

                                                 package = "lineagespot"),

                       gff3_path = system.file("extdata",

@@ -8,8 +8,7 @@ lineagespot_hits(

   vcf_table = NULL,

   ref_folder = NULL,

   voc = c("B.1.617.2", "B.1.1.7", "B.1.351", "P.1"),

-  file.out = paste0("lineage_hits_", Sys.Date(), ".txt"),

-  print.out = FALSE

+  file.out = paste0("lineage_hits_", Sys.Date(), ".txt")

 )

 }

 \arguments{

@@ -20,8 +19,6 @@ lineagespot_hits(

 \item{voc}{A character vector containing the names of the lineages of interest}

 \item{file.out}{Given name for the output file}

-

-\item{print.out}{Logical value indicating if the produced table should be printed}

 }

 \value{

 A data table containing all identified SARS-CoV-2 variants

@@ -33,7 +30,7 @@ coming from outbreak.info reports

 }

 \examples{

-variants_table = merge_vcf(vcf_folder = system.file("extdata",

+variants_table <- merge_vcf(vcf_folder = system.file("extdata",

                                                     "vcf-files",

                                                     package = "lineagespot"),

@@ -43,12 +40,12 @@ variants_table = merge_vcf(vcf_folder = system.file("extdata",

 # retrieve lineage reports using outbreak.info's API

-lineage_hits_table = lineagespot_hits(vcf_table = variants_table,

+lineage_hits_table <- lineagespot_hits(vcf_table = variants_table,

                                       voc = c("B.1.1.7", "B.1.617.2"))

 # use user-specified references

-lineage_hits_table.2 = lineagespot_hits(vcf_table = variants_table,

+lineage_hits_table.2 <- lineagespot_hits(vcf_table = variants_table,

                                         ref_folder = system.file("extdata", "ref",

                                                                  package = "lineagespot"))

@@ -8,8 +8,7 @@ merge_vcf(

   vcf_fls = NULL,

   vcf_folder = NULL,

   gff3_path = NULL,

-  file.out = paste0("Variant_table_", Sys.Date(), ".txt"),

-  print.out = FALSE

+  file.out = paste0("Variant_table_", Sys.Date(), ".txt")

 )

 }

 \arguments{

@@ -21,8 +20,6 @@ will be integrated into a single table}

 \item{gff3_path}{Path to GFF3 file}

 \item{file.out}{Given name for the output file}

-

-\item{print.out}{Logical value indicating if the produced table should be printed}

 }

 \value{

 A data table contaiing all variants from each sample of the input VCF files

@@ -7,8 +7,7 @@

 uniq_variants(

   hits_table = NULL,

   AF_threshold = 0.8,

-  file.out = paste0("lineage_report_", Sys.Date(), ".txt"),

-  print.out = FALSE

+  file.out = paste0("lineage_report_", Sys.Date(), ".txt")

 )

 }

 \arguments{

@@ -20,8 +19,6 @@ identify the presence or not of a variant. This is used to compute the number

 of variants in a sample and eventually the proportion of a lineage.}

 \item{file.out}{Given name for the output file}

-

-\item{print.out}{Logical value indicating if the produced table should be printed}

 }

 \value{

 A data table with metrics assessing the

@@ -32,16 +29,16 @@ Lineage report for variants overlapping

 }

 \examples{

-variants_table = merge_vcf(vcf_folder = system.file("extdata", "vcf-files",

+variants_table <- merge_vcf(vcf_folder = system.file("extdata", "vcf-files",

                                                     package = "lineagespot"),

                            gff3_path = system.file("extdata",

                                                    "NC_045512.2_annot.gff3",

                                                    package = "lineagespot"))

-lineage_hits_table = lineagespot_hits(vcf_table = variants_table,

+lineage_hits_table <- lineagespot_hits(vcf_table = variants_table,

                                       voc = c("B.1.1.7", "B.1.617.2"))

-report = uniq_variants(hits_table = lineage_hits_table)

+report <- uniq_variants(hits_table = lineage_hits_table)

 head(report)

 }

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